from ast import literal_eval
from typing import Dict, Optional, Sequence, Tuple, Union
import pandas as pd
from anndata import AnnData
from spatialtis.config import CONFIG
from spatialtis.console import console
def writer_verbose(key, part: str = "uns", verbose: Optional[bool] = None):
if verbose is None:
verbose = CONFIG.VERBOSE
if verbose:
console.print(f":package: [green]Added to AnnData, {part}: [bold cyan]'{key}'")
def df2adata_uns(
df: pd.DataFrame,
adata: AnnData,
key: str,
params: Optional[Dict] = None,
verbose: Optional[bool] = None,
):
"""Write pandas.DataFrame with parameters to `AnnData.uns`
The `AnnData` haven't fully support read/write of a `pandas.Dataframe` object,
this is a temporal solution to store it in a `Dict`
The meaning of each key:
- **df**: The dataframe itself
- **iname**: The name of index/MultiIndex
- **colname**: The name of columns/MultiIndex
- **params**: The parameters
Args:
df: The `pandas.DataFrame` object you want to write to the `AnnData.uns` field
adata: The AnnData object for storage
key: Which key in `AnnData.obs` key you want to write
params: Add parameters
verbose: Control the verbosity
"""
container = dict(
df=str(df.to_dict()), iname=df.index.names, colname=list(df.columns.names),
)
if params is not None:
container["params"] = params
adata.uns[key] = container
writer_verbose(key, verbose=verbose)
def col2adata_obs(
col: Sequence, adata: AnnData, key: str, verbose: Optional[bool] = None
):
"""Write an array to `AnnData.obs`
Args:
col: An array-like object that add to `AnnData.obs`
adata: The `AnnData` object for storage
key: Which key in `AnnData.obs` key you want to write
verbose: Control the verbosity
"""
adata.obs[key] = col
writer_verbose(key, "obs", verbose=verbose)
[docs]def get_result(
adata: AnnData, key: str, params: bool = False,
) -> Union[pd.DataFrame, Tuple[pd.DataFrame, Dict]]:
"""Read spatialtis result from `AnnData.uns` as `pandas.DataFrame` object
To get the params, use `params=True`
Args:
adata: The `AnnData` object for storage
key: Which key in `AnnData.uns` you want to read
params: Whether to return parameters
"""
container = adata.uns[key]
df = pd.DataFrame(literal_eval(container["df"]))
df.index.set_names(container["iname"], inplace=True)
df.columns.set_names(container["colname"], inplace=True)
if params:
return df, container["params"]
else:
return df
